I received feedback from my report I’d sent to Apple (Yay, they do work!). They pointed out that the issue was due to a third party app I have installed called Disk Drill by CleverFiles (which I have as part of my Setapp subscription). The app has a “feature” called Guaranteed Recovery that is supposed to help recover files later if you accidentally delete them. It “works” by creating thousands of hard links to what appears to be every file on your system in a hidden directory (/System/Volumes/Data/.cleverfiles/). This means when you delete a file, it’s not really deleted because there’s a hard link effectively creating a duplicate in the hidden folder.

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Over the last month or so, I’ve been trying to free up space on my main SSD because the OS is constantly complaining that my drive is full. Because I kept getting alerts that I needed more free space, I kept moving/deleting files. Eventually I’d cleared/off-loaded over 500G of data and was still scraping by with about 30G of free space. Now that I’m aware of the issue, I’ve taken a look into the .cleverfiles hidden folder on my iMac and I see it has over 450G in it. Wow.

Wow indeed. First, the hidden folder should be excluded from Time Machine. And second, it seems like there’s a bug where it isn’t being pruned automatically.